rcellosaurus: Cellosaurus for R

The goal of rcellosaurus is to provide some convenience functions for accessing the Cellosaurus dataset in R. Cellosaurus is a knowledge resource on cell lines. This R package is not associated with Cellosaurus, and the good people at Cellosaurus are not responsible for it in any way.

Installation

devtools::install_github("jimvine/rcellosaurus")

Use

First download the XML version of the Cellosaurus dataset:

ftp://ftp.expasy.org/databases/cellosaurus

Load that into R with read_cellosaurus_xml() and extract a nodeset containing all the cell-line elements:

cellosaurus <- read_cellosaurus_xml("data/cellosaurus.xml")
cell_lines <- cell_lines_all(cellosaurus)

(where data is the path to the folder where you have stored the downloaded dataset.)

To find a cell-line and identify the sex according to the Cellosaurus record use the following:

CVCL_E548 <- cell_lines_filter(cell_lines,
                               filter_by = "accession",
                               filter_term = "CVCL_E548",
                               filter_type = "equals")

cell_line_sex(CVCL_E548)

Or simply nest these functions to get the sex directly:

cell_line_sex(cell_lines_filter(cell_lines,
                                filter_by = "accession",
                                filter_term = "CVCL_E548",
                                filter_type = "equals"))

The rcellosaurus package is powered by the xml2 package, so returned results are typically XML nodes or nodesets that can be further processed using xml2 if desired.

References

Bairoch A. The Cellosaurus: a cell line knowledge resource. http://web.expasy.org/cellosaurus/